Structure of PDB 3goc Chain B Binding Site BS02

Receptor Information

>3goc Chain B (length=228) Species: 227882 (Streptomyces avermitilis MA-4680 = NBRC 14893)

TTVRIPAGWPATEEEARAVQDELRGRVILDEPGPPPGTGRVTGVDVAYDD
ERDVVVAAAVVLDAATLDVVAEATAVGEVSFPYVPGLLAFREIPTVLAAL
DALPCPPGLIVCDGYGVAHPRRFGLASHLGVLTGLPTIGVAKNPFTFSYE
DPGAPRGSAAPLLAGADEVGRALRTQSGVKPVFVSVGHRVDLDHACAHTL
ALTPKYRIPETTRRADSLCRRALKEATA

Ligand information

• Ligand ID: MG
• InChI: InChI=1S/Mg/q+2
• InChIKey: JLVVSXFLKOJNIY-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mg+2]
  CACTVS 3.341: [Mg++]
• Formula: Mg
• Name: MAGNESIUM ION
• DrugBank: DB01378
• PDB chain: 3goc Chain B Residue 302

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3goc Crystal structure of the Endonuclease V (SAV1684) from Streptomyces avermitilis. Northeast Structural Genomics Consortium Target SvR196.
• Resolution: 1.6 Å
• Binding residue (original residue number in PDB): D46 D114
• Binding residue (residue number reindexed from 1): D45 D113
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 3.1.21.7: deoxyribonuclease V.

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0003727 single-stranded RNA binding
• GO:0004519 endonuclease activity
• GO:0016891 RNA endonuclease activity, producing 5'-phosphomonoesters
• GO:0043737 deoxyribonuclease V activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006281 DNA repair

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:3goc, PDBe:3goc, PDBj:3goc
• PDBsum: 3goc
• UniProt: Q82MH6|NFI_STRAW Endonuclease V (Gene Name=nfi)